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AvogadroLibs
1.95.1
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This is the complete list of members for Molecule, including all inherited members.
| addAtom(unsigned char atomicNumber) override | Molecule | virtual |
| addAtom(unsigned char atomicNumber, Index uniqueId) | Molecule | virtual |
| addAtom(unsigned char number, Vector3 position3d, Index uniqueId=MaxIndex) (defined in Molecule) | Molecule | |
| addAtom(unsigned char atomicNumber, Vector3 position3d) (defined in Molecule) | Molecule | |
| addBond(const AtomType &a, const AtomType &b, unsigned char bondOrder=1) override | Molecule | virtual |
| addBond(Index atomId1, Index atomId2, unsigned char bondOrder=1) override | Molecule | virtual |
| addBond(const AtomType &a, const AtomType &b, unsigned char bondOrder, Index uniqueId) | Molecule | virtual |
| addBond(Index atomId1, Index atomId2, unsigned char bondOrder, Index uniqueId) | Molecule | virtual |
| addBonds(const Core::Array< std::pair< Index, Index >> &bonds, const Core::Array< unsigned char > &orders) (defined in Molecule) | Molecule | |
| addCube() | Molecule | |
| Added enum value | Molecule | |
| addMesh() | Molecule | |
| addResidue(std::string &name, Index &number, char &id) (defined in Molecule) | Molecule | |
| addResidue(Residue &residue) (defined in Molecule) | Molecule | |
| atom(Index index) const | Molecule | |
| atomByUniqueId(Index uniqueId) | Molecule | |
| atomCount() const | Molecule | |
| atomCount(unsigned char atomicNumber) const | Molecule | |
| atomicNumber(Index atomId) const | Molecule | |
| atomicNumbers() const | Molecule | |
| atomPosition2d(Index atomId) const | Molecule | |
| atomPosition3d(Index atomId) const | Molecule | |
| atomPositions2d() const | Molecule | |
| atomPositions2d() | Molecule | |
| atomPositions3d() const | Molecule | |
| atomPositions3d() | Molecule | |
| Atoms enum value | Molecule | |
| atomSelected(Index atomId) const | Molecule | |
| AtomType typedef | Molecule | |
| atomUniqueId(const AtomType &atom) const | Molecule | |
| atomUniqueId(Index atom) const | Molecule | |
| atomUniqueIds() (defined in Molecule) | Molecule | |
| basisSet() | Molecule | |
| basisSet() const (defined in Molecule) | Molecule | |
| bestFitPlane() const | Molecule | |
| bestFitPlane(const Array< Vector3 > &pos) | Molecule | static |
| bond(Index index) const | Molecule | |
| bond(const AtomType &a, const AtomType &b) const | Molecule | |
| bond(Index atomId1, Index atomId2) const | Molecule | |
| bondByUniqueId(Index uniqueId) | Molecule | |
| bondCount() const | Molecule | |
| bondOrder(Index bondId) const | Molecule | |
| bondOrders() const | Molecule | |
| bondPair(Index bondId) const | Molecule | |
| bondPairs() const | Molecule | |
| Bonds enum value (defined in Molecule) | Molecule | |
| bonds(const AtomType &a) | Molecule | |
| bonds(Index a) | Molecule | |
| bonds(Index a) const | Molecule | |
| BondType typedef | Molecule | |
| bondUniqueId(const BondType &bond) const | Molecule | |
| bondUniqueId(Index bond) const | Molecule | |
| bondUniqueIds() (defined in Molecule) | Molecule | |
| centerOfGeometry() const | Molecule | |
| centerOfMass() const | Molecule | |
| changed(unsigned int change) | Molecule | signal |
| clearAtoms() | Molecule | virtual |
| clearBonds() | Molecule | virtual |
| clearCubes() (defined in Molecule) | Molecule | |
| clearMeshes() (defined in Molecule) | Molecule | |
| color(Index atomId) const | Molecule | |
| colors() | Molecule | |
| colors() const | Molecule | |
| composition() const | Molecule | |
| coordinate3d(int index) const (defined in Molecule) | Molecule | |
| coordinate3dCount() (defined in Molecule) | Molecule | |
| cube(Index index) (defined in Molecule) | Molecule | |
| cube(Index index) const (defined in Molecule) | Molecule | |
| cubeCount() const (defined in Molecule) | Molecule | |
| cubes() | Molecule | |
| cubes() const (defined in Molecule) | Molecule | |
| CustomElementMap typedef | Molecule | |
| customElementMap() const | Molecule | |
| data(const std::string &name) const | Molecule | |
| dataMap() const | Molecule | |
| dataMap() | Molecule | |
| emitChanged(unsigned int change) | Molecule | slot |
| findAtomUniqueId(Index index) const (defined in Molecule) | Molecule | |
| findBondUniqueId(Index index) const (defined in Molecule) | Molecule | |
| forceVector(Index atomId) const | Molecule | |
| forceVectors() const | Molecule | |
| forceVectors() | Molecule | |
| formalCharge(Index atomId) const | Molecule | |
| formalCharges() | Molecule | |
| formalCharges() const | Molecule | |
| formula(const std::string &delimiter="", int showCountsOver=1) const | Molecule | |
| getAtomBonds(Index index) const (defined in Molecule) | Molecule | |
| getAtomOrders(Index index) const (defined in Molecule) | Molecule | |
| getAtomsAtLayer(size_t layer) (defined in Molecule) | Molecule | |
| graph() const | Molecule | |
| hallNumber() const | Molecule | |
| hasCustomElements() const | Molecule | |
| hasData(const std::string &name) const | Molecule | |
| hybridization(Index atomId) const | Molecule | |
| hybridizations() | Molecule | |
| hybridizations() const | Molecule | |
| isSelectionEmpty() const | Molecule | |
| label(Index atomId) const (defined in Molecule) | Molecule | |
| layer(Index atomId) const (defined in Molecule) | Molecule | |
| layer() (defined in Molecule) | Molecule | |
| layer() const (defined in Molecule) | Molecule | |
| m_basisSet (defined in Molecule) | Molecule | protected |
| m_colors (defined in Molecule) | Molecule | protected |
| m_coordinates3d (defined in Molecule) | Molecule | protected |
| m_cubes (defined in Molecule) | Molecule | protected |
| m_customElementMap (defined in Molecule) | Molecule | protected |
| m_data (defined in Molecule) | Molecule | protected |
| m_forceVectors (defined in Molecule) | Molecule | protected |
| m_formalCharges (defined in Molecule) | Molecule | protected |
| m_hallNumber (defined in Molecule) | Molecule | protected |
| m_hybridizations (defined in Molecule) | Molecule | protected |
| m_label (defined in Molecule) | Molecule | protected |
| m_meshes (defined in Molecule) | Molecule | protected |
| m_positions2d (defined in Molecule) | Molecule | protected |
| m_positions3d (defined in Molecule) | Molecule | protected |
| m_residues (defined in Molecule) | Molecule | protected |
| m_selectedAtoms (defined in Molecule) | Molecule | protected |
| m_timesteps (defined in Molecule) | Molecule | protected |
| m_unitCell (defined in Molecule) | Molecule | protected |
| m_vibrationFrequencies (defined in Molecule) | Molecule | protected |
| m_vibrationIntensities (defined in Molecule) | Molecule | protected |
| m_vibrationLx (defined in Molecule) | Molecule | protected |
| makeBondPair(const Index &a, const Index &b) (defined in Molecule) | Molecule | static |
| mass() const | Molecule | |
| mesh(Index index) (defined in Molecule) | Molecule | |
| mesh(Index index) const (defined in Molecule) | Molecule | |
| meshCount() const (defined in Molecule) | Molecule | |
| Modified enum value (defined in Molecule) | Molecule | |
| Molecule(QObject *parent_=nullptr) (defined in Molecule) | Molecule | |
| Molecule(const Molecule &other) | Molecule | |
| Molecule(const Core::Molecule &other) | Molecule | |
| Avogadro::Core::Molecule::Molecule() | Molecule | |
| Avogadro::Core::Molecule::Molecule(Molecule &&other) noexcept | Molecule | |
| MoleculeChange enum name | Molecule | |
| NoChange enum value | Molecule | |
| operator=(const Molecule &other) | Molecule | |
| operator=(const Core::Molecule &other) | Molecule | |
| Avogadro::Core::Molecule::operator=(Molecule &&other) noexcept | Molecule | |
| perceiveBondsFromResidueData() | Molecule | |
| perceiveBondsSimple(const double tolerance=0.45, const double minDistance=0.32) | Molecule | |
| PersistentAtomType typedef | Molecule | |
| PersistentBondType typedef | Molecule | |
| radius() const | Molecule | |
| removeAtom(Index index) override | Molecule | virtual |
| removeAtom(const AtomType &atom) override | Molecule | virtual |
| removeBond(Index index) override | Molecule | virtual |
| removeBond(const BondType &bond) override | Molecule | virtual |
| removeBond(const AtomType &atom1, const AtomType &atom2) override | Molecule | virtual |
| removeBond(Index atom1, Index atom2) override | Molecule | virtual |
| removeBonds(Index atom) (defined in Molecule) | Molecule | |
| Removed enum value (defined in Molecule) | Molecule | |
| residue(Index index) (defined in Molecule) | Molecule | |
| residueCount() const | Molecule | |
| residues() (defined in Molecule) | Molecule | |
| residues() const (defined in Molecule) | Molecule | |
| setAtomicNumber(Index atomId, unsigned char atomicNumber) | Molecule | |
| setAtomicNumbers(const Core::Array< unsigned char > &nums) | Molecule | |
| setAtomPosition2d(Index atomId, const Vector2 &pos) | Molecule | |
| setAtomPosition3d(Index atomId, const Vector3 &pos) | Molecule | |
| setAtomPositions2d(const Core::Array< Vector2 > &pos) | Molecule | |
| setAtomPositions3d(const Core::Array< Vector3 > &pos) | Molecule | |
| setAtomSelected(Index atomId, bool selected) | Molecule | |
| setBasisSet(BasisSet *basis) | Molecule | |
| setBondOrder(Index bondId, unsigned char order) | Molecule | |
| setBondOrders(const Array< unsigned char > &orders) | Molecule | |
| setBondPair(Index bondId, const std::pair< Index, Index > &pair) | Molecule | |
| setBondPairs(const Array< std::pair< Index, Index >> &pairs) | Molecule | |
| setColor(Index atomId, Vector3ub color) | Molecule | |
| setColors(const Core::Array< Vector3ub > &colors) | Molecule | |
| setCoordinate3d(int coord) (defined in Molecule) | Molecule | |
| setCoordinate3d(const Array< Vector3 > &coords, int index) (defined in Molecule) | Molecule | |
| setCustomElementMap(const CustomElementMap &map) | Molecule | |
| setData(const std::string &name, const Variant &value) | Molecule | |
| setDataMap(const VariantMap &map) | Molecule | |
| setForceVector(Index atomId, const Vector3 &force) | Molecule | |
| setForceVectors(const Core::Array< Vector3 > &forces) | Molecule | |
| setFormalCharge(Index atomId, signed char charge) | Molecule | |
| setFormalCharges(const Core::Array< signed char > &charges) | Molecule | |
| setHallNumber(unsigned short hallNumber) | Molecule | |
| setHybridization(Index atomId, AtomHybridization hybridization) | Molecule | |
| setHybridizations(const Core::Array< AtomHybridization > &hybs) | Molecule | |
| setLabel(const Core::Array< std::string > &label) (defined in Molecule) | Molecule | |
| setLabel(Index atomId, const std::string &label) (defined in Molecule) | Molecule | |
| setLayer(Index atomId, size_t layer) (defined in Molecule) | Molecule | |
| setTimeStep(double timestep, int index) | Molecule | |
| setUnitCell(UnitCell *uc) | Molecule | |
| setVibrationFrequencies(const Array< double > &freq) (defined in Molecule) | Molecule | |
| setVibrationIntensities(const Array< double > &intensities) (defined in Molecule) | Molecule | |
| setVibrationLx(const Array< Array< Vector3 >> &lx) (defined in Molecule) | Molecule | |
| swapAtom(Index a, Index b) (defined in Molecule) | Molecule | |
| swapBond(Index a, Index b) (defined in Molecule) | Molecule | |
| timeStep(int index, bool &status) (defined in Molecule) | Molecule | |
| undoMolecule() (defined in Molecule) | Molecule | |
| UnitCell enum value (defined in Molecule) | Molecule | |
| unitCell() | Molecule | |
| unitCell() const | Molecule | |
| vibrationFrequencies() const (defined in Molecule) | Molecule | |
| vibrationIntensities() const (defined in Molecule) | Molecule | |
| vibrationLx(int mode) const (defined in Molecule) | Molecule | |
| ~Molecule() override | Molecule | virtual |
1.8.14